More than half of the city’s 50 most popular restaurants were cited last year by health inspectors for stomach-churning violations that included evidence of mice, flies and roaches.

At least 29 of the Zagat survey’s top-50 most popular New York restaurants were found to be in need of some serious scrubbing and vermin control by the city Department of Health – including Danny Meyer’s Gramercy Tavern, Union Square landmark Blue Water Grill and French legend Le Bernardin.

And hot spots Balthazar and Lupa were just one small infraction away from flunking inspection and forcing DOH officials to come back for a follow-up visit to decide if the famed eateries should be shut down.

This year, lovebirds may think twice about experiencing Zagat’s “ultimate romantic night out” at One If By Land, Two If By Sea after reading DOH’s inspection report.

Evidence of two non-human species – flies and mice – were found at the Greenwich Village restaurant, where Mayor Bloomberg once hinted he’d like to take apple-of-his-eye Jennifer Lopez.

TriBeCa landmark Chanterelle, winner of the outstanding restaurant prize at last year’s James Beard Foundation Awards, is famous for its huge windows, vast cheese plate and A-list clientele.

But Susan Sarandon likely didn’t get the lowdown on the restaurant’s basement, where 15 to 20 mice droppings were found, before she threw a party there in November for the likes of Penelope Cruz.

At David Bouley’s wildly popular Danube, five roaches were found milling about in the basement.

Insects and rodents weren’t the only findings.

At Craft, Danube, Balthazar and Blue Ribbon, cold food was found at temperatures above 41 degrees, making it friendly to a host of dangerous germs.

At Café Des Artistes, Asia de Cuba and Chanterelle, canned foods were found “swollen, leaking rusted or severely dented.”

Under the city health code, points are given to a restaurant depending on the type of violation. Unless an eatery receives 28 points or more, the restaurant passes inspection and no follow-up inspection is required.

Roseanne Manetta, general manager at One If By Land, noted that the wine cellar where the mice droppings were found “is three levels below the kitchen,” adding that an exterminator caught two or three mice in October.

Chanterelle owner Karen Waltuck claimed there was no way to know when the rodent did its business.

“It might have been 10 years ago,” Waltuck claimed.

Additional reporting by Lindsay Powers

Restaurant Date of InspectViolation(s)

Lupa 8/23/04 flying insect activity present

Cesca 8/03/04 flying insect activity present

Blue Water Grill 8/26/04 flying insect activity present

Chanterelle 3/02/04 15-20 fresh mice droppings noted on floor

Felidia 11/09/04 20 fresh mice excreta observed on floor

One if by Land Two if by Sea 9/20/04 mouse activity present in that 12 fresh mice excreta observed on floor

Gramercy Tavern 7/14/04 food not protected at all times from potential sources of contamination

Danube 8/18/04 FIVE live roaches observed crawling on wall

Balthazar 2/10/04 food not protected at all times from potential sources of contamination